Snippets

osimis Compress a DICOM files with various compression type

Created by Alain Mazy
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#!/bin/bash
# this script creates transcode a DICOM file with all types of compression.
# it creates one study per compression type
#
# note: it has been tested only  only on Windows: you would probably just need to update dcmodify into ./dcmodify and gdcmconv into ./gdcmconv to make it work on Linux
# prerequisites:
# you must have DCMTK installed and in your path [http://dicom.offis.de/dcmtk.php.en]
# you must have GDCM installed and in your path [https://github.com/malaterre/GDCM/releases]

sourceFile=$1

function convertInstance {
	sourceFile=$1
	studyId=$2
	formatName=$3
	gdcmOptions=$4
	target=$1_$3
	
	echo "convertInstanceing to $formatName"
	cp -f $1 tmp_$target
	dcmodify --no-backup -gin -gse --modify "(0020,000d)=$studyId" --modify "(0008,1030)=$formatName"  --insert "(0008,103e)=$formatName" tmp_$target
	gdcmconv $gdcmOptions -U -i tmp_$target -o $target
	rm tmp_$target
}  

function convertInstanceFile {
	sourceFile=$1

	convertInstance $1 1 raw "--raw"
	convertInstance $1 2 jpeg "--jpeg"
	convertInstance $1 3 jpegls "--jpegls"
	convertInstance $1 4 rle "--rle"
	convertInstance $1 5 jp2k "--j2k"
	convertInstance $1 6 jp2klossy100 "--j2k --lossy -q 100"
	convertInstance $1 7 jp2klossy90 "--j2k --lossy -q 90"
	convertInstance $1 8 jp2klossy80 "--j2k --lossy -q 80"
	convertInstance $1 9 jp2klossy75 "--j2k --lossy -q 75"
	convertInstance $1 10 jp2klossy70 "--j2k --lossy -q 70"
	convertInstance $1 11 jp2klossy65 "--j2k --lossy -q 65"
	convertInstance $1 12 jp2klossy60 "--j2k --lossy -q 60"
	convertInstance $1 13 jp2klossy50 "--j2k --lossy -q 50"
}

convertInstanceFile $sourceFile


# Orthanc does not accept those: convertInstance $1 gzip "--deflated"

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